Methods are known for comparing the amino acid sequences of proteins to identify indel (insertion/deletion) associated sequences. Such methods are described for use in identifying peptides, peptide analogs, and peptidomimetics that have a high probability of modulating or mimicking the activity of a target protein. For example, in PCT international patent application publication no. WO 97/01578, methods are described for identifying molecules that affect biological activity of a target protein in which information regarding the location of an indel in a target protein is used to identify nearby fragments.
Protozoan pathogens are responsible for a wide variety of disease, typically tropical in nature. These pathogens exist as intracellular parasites in a host and include organisms that appear to be protozoan in nature such as Pneumocystis. An example of such protozoan pathogens is the genus Leishmania, which causes a spectrum of tropical and subtropical diseases known as the leishmaniases. These consist of several forms including cutaneous, mucocutaneous, visceral and diffuse cutaneous leishmaniasis. The incidence of such tropical diseases has been on the rise due to multiple factors including the AIDS epidemic, increased international travel, lack of effective vaccines, difficulty in controlling vectors, and the development of resistance to chemotherapy.
Leishmania live as either extracellular, flagellated promastigotes in the digestive tract of their sand fly vector or as non-flagellated amastigotes within macrophages where they survive and replicate within phagolysosomes. During both the innate and acquired immune responses, macrophages respond to extracellular signals to become activated for enhanced antimicrobial activity. This is a critical requirement leading to the elimination of intracellular pathogens. However, recent findings have shown that leishmania and other intracellular pathogens have developed mechanisms to interfere with cell signaling pathways thereby preventing macrophages from becoming effectively activated [Reiner N E. (1994) Immunol. Today 15:374-381; Nandan, D. et al. (2000) J Leukocyte Biology 67:464-470]. As a result, these organisms are able to survive and successfully multiply within the otherwise hostile intracellular milieu of macrophages. L. donovani is the major causative agent of human visceral leishmaniasis. This disease is progressive and often fatal if untreated. Recently, it has been shown that macrophages infected with L. donovani show a phenotype of impaired cell signaling and cell deactivation. For example, interferon-γ signaling through the Jak-Stat1 pathway [Nandan D. and Reiner N E. (1995) Infect. Immun. 63:4495-4500] and mitogen-activated protein kinase signaling leading to iNOS induction and c-FOS expression were observed to be markedly attenuated in leishmania infected cells [Nandan D. et al. (I 999) Infection and Immunity 67:4055-4063]. Of significant interest was the finding that the deactivated phenotype was reversed in cells that had been incubated with the protein tyrosine phosphatase (PTP) inhibitor sodium orthovandate prior to infection [Nandan D. et al. (1999) Infection and Immunity 67:4055-4063]. Several lines of evidence have recently converged to demonstrate a role for the Src-homology 2 (SH2) domain containing protein tyrosine phosphatase-1 (SHP-1) in the pathogenesis of infections with leishmania [Nandan D. et al. (1999) Infection and Immunity 67:4055-4063; Olivier M. et al. (1998) J. Biol. Chem. 273:13944-13949; Blanchette J. et al. (1999) Eur. J Immunol. 29:3737-3744; Forget G. et al. (1999) Journal of Leukocyte Biology Supplement 31:1999]. In particular, SHP-1 has been shown to become activated in leishmania infected cells [Nandan D. et al. (1999) Infection and Immunity 67:4055-4063; 6] and leishmania infection is attenuated under conditions of SHP-1 deficiency [Forget G. et al. (1999) Journal of Leukocyte Biology Supplement 31:1999]. Moreover, it has recently been shown that a conventional anti-leishmanial agent used clinically, sodium stibogluconate, is an inhibitor of SHP-1 [Pathak M K. and Yi T. (2001) J Immunol. 167:3391-3397].